If your store carries items that are fulfilled somewhere else, you need to add shipping costs for those products independently on Shopify's end.
In situations where your client has both Supliful and non-Supliful items in their cart, Shopify will naturally take the most reduced shipping rate accessible from both item gatherings and join them together into one. That way your client will see one delivery alternative available at the checkout.
In case you wish to make more advanced shipping rate combinations, there are quite a few shipping applications available in the Shopify App Store.